1. Minutes of the last meeting

2. Software Development

2.1 Applications

Alan has extended amino acid property calculations to use
monoisotopic molecular weights in addition to the current average
weights. Monoisotopic weights are used in analysis of mass spec
data. The embProp functions now read a new file Emolwt.dat and pass
new objects EmbPPropAmino and EmbPPropMolwt. A command line switch
-mono is now added to all programs that use this local data file.

The local data files need comments added to their headers to describe
the source of the data values.

Alan has added a new application density to report and
plot high and low densities for individual bases (-quad) and AT+GC
(-dual) as requested by Tim Carver at Sanger.

Alan has made very general wrappers for the emira and
emiraest integration which could be used for other
applications.

Peter has modified pepcoil to produce a report as
output. This included extensions to the "motif" report format. To
give a clean output by default non coiled-coil regions are not
reported. The frames are reported as additional columns. In the
"motif" format these appear only if a frame is set by the program. In
table formats the frame columns appear with missing ('.') values.

2.2 Libraries

Peter has further updated GFF3 output to require a reading
frame for coding sequence features. This included adding a new
function to identify CDS features using the Sequence Ontology
internal code. Similar functions can be added for other feature classes.

Peter has corrected the meaning of "Case" in function names for
string processing so that it always refers to case-insensitive
processing. For some functions the naming was inconsistent.

Mahmut has identified applications suitable for generating
DASGFF annotations. To fit with current servers, these need to accept
a sequence as the only input, for example applications which search
for matches to a standard database of motifs such as prosite, jaspar
or transfac. This excludes applications such as fuzzpro which
need a user-defined pattern.

Peter identified a need for a new output report attribute to
indicate whether features are over the entire sequence or are for
regions with specific properties. The whole: attribute can be
used for applications such as dan which report all windows over
the sequence. Such applications are of little interest as DASGFF
annotation servers.

Mahmut has found further references to XML feature and sequence
formats. None have a recommended standard, although AGAVE is top of a
list from Peter Ernst (DKFZ).

Mahmut noted that DASGFF format includes the concept of a feature
group where related features (e.g. a set of features for a single
transcript/gene) have a common group name with
annotation. Peter will look into reading DASGFF as input and
preserving the group annotation in the feature table so that it can be
reproduced on output.

Mahmut will circulate links to DAS2 applications, including
IGB.

Mahmut asked whether object files could be built in a
subdirectory as they are appearing in eclipse in the list of files (or
perhaps there is a way to filter them out in eclipse) and whether
large source files (over 10,000 lines) could be split as they can be
slow to scroll in eclipse in C++ mode.

2.3 SoapLab

Mahmut found a problem with the AppLab server
running estgenome
with large input sequences. The problem was fixed by killing the jobs
after more than 12 hours. We have a new version of LSF installed so
the server will be able to run jobs in batch again.

2.4 Other development

A user has produced an emacs mode for editing ACD files. Alan
has contacted him to merge in the EMBOSS C style. This is now being
tested. It may be necessary to reintroduce the automatic brace insertion.

3. Administration

3.1 Release 5.0.0

Alan is waiting for confirmation of the fix for
the primer3_core launch problem on Windows.

Alan will rebuild on Windows with the 3 new applications added
since the release.

4. Documentation and Training

4.1 Books

Jon has committed the latest revisions of guidelines for the
documentation of applications and source code, and has added details
of user-defined values for ACD data types such as lists.

5. User queries and answers

Jon noted that we still need to update the list of applications
required to describe those already available elsewhere (FASTA and
BLAST) and to remove some that are already in EMBOSS.